A protocols::moves::Mover that packs the side-chains (very similar to pack_missing_sidechains() More...

#include <RepackSidechainsMover.hh>

Inheritance diagram for protocols::minimization_packing::RepackSidechainsMover:

Public Types
typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Public Member Functions
	RepackSidechainsMover ()
	default constructor More...

	RepackSidechainsMover (ScoreFunctionCOP scorefxn)
	constructor with typename More...

	RepackSidechainsMover (RepackSidechainsMover const &other)

void	apply (Pose &pose) override
	Main Method. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

void	parse_my_tag (TagCOP, basic::datacache::DataMap &) override
	parse XML (specifically in the context of the parser/scripting scheme) More...

virtual void	parse_score_function (TagCOP, basic::datacache::DataMap const &)
	parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...

protocols::moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme More...

void	set_scorefxn (ScoreFunctionCOP sf)

ScoreFunctionCOP	scorefxn () const

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Attributes
ScoreFunctionCOP	scorefxn_

Additional Inherited Members
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

A protocols::moves::Mover that packs the side-chains (very similar to pack_missing_sidechains()

Member Typedef Documentation

typedef core::scoring::ScoreFunctionCOP protocols::minimization_packing::RepackSidechainsMover::ScoreFunctionCOP

Constructor & Destructor Documentation

protocols::minimization_packing::RepackSidechainsMover::RepackSidechainsMover ( )

default constructor

protocols::minimization_packing::RepackSidechainsMover::RepackSidechainsMover ( ScoreFunctionCOP scorefxn )

constructor with typename

Constructs a RepackSidechainsMover with PackerTask <task> evaluated using <scorefxn>

ScoreFunction scorefxn /function to minimize while changine rotamers PackerTask task /object specifying what to design/pack core::Size (int) nloop /number of loops in the Pose (???)

protocols::minimization_packing::RepackSidechainsMover::RepackSidechainsMover ( RepackSidechainsMover const & other )

References scorefxn(), and scorefxn_.

Member Function Documentation

void protocols::minimization_packing::RepackSidechainsMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pack::task::TaskFactory::create_packer_task(), core::pack::figure_out_repackable_residues(), core::pose::initialize_atomid_map(), core::pack::pack_rotamers(), and scorefxn_.

protocols::moves::MoverOP protocols::minimization_packing::RepackSidechainsMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::minimization_packing::RepackSidechainsMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::minimization_packing::RepackSidechainsMover::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References protocols::minimization_packing::RepackSidechainsMoverCreator::mover_name().

void protocols::minimization_packing::RepackSidechainsMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::moves::Mover.

References parse_score_function().

void protocols::minimization_packing::RepackSidechainsMover::parse_score_function	(	TagCOP	tag,
		basic::datacache::DataMap const &	datamap
	)

virtual

parse "scorefxn" XML option (can be employed virtually by derived Packing movers)

References core::scoring::parse_score_function(), and set_scorefxn().

Referenced by parse_my_tag().

ScoreFunctionCOP protocols::minimization_packing::RepackSidechainsMover::scorefxn ( ) const

inline

Referenced by RepackSidechainsMover().

void protocols::minimization_packing::RepackSidechainsMover::set_scorefxn ( ScoreFunctionCOP sf )

References scorefxn_.

Referenced by parse_score_function().

Member Data Documentation

ScoreFunctionCOP protocols::minimization_packing::RepackSidechainsMover::scorefxn_

private

Referenced by apply(), RepackSidechainsMover(), and set_scorefxn().

The documentation for this class was generated from the following files:

src/protocols/minimization_packing/RepackSidechainsMover.hh
src/protocols/minimization_packing/RepackSidechainsMover.cc

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation